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After reading the Google Chrome book, it is a long time waiting for it to be released for Linux….

Also, I’m looking forward for the plugins to enhance Chrome. Although it did import my settings/passwords(?!)/bookmarks from Firefox, but it has no Foxmarks, AdBlock and some other goodies I’m now used to on all the computers I regularly use.

I’m now registered in both systems (and getting “verified” in CS), and so far I stayed with three people (at two places) found via HC and CS. Both experiences were highly positive. Actually, my world outlook changed quite a bit after my first stay: I heard from someone that

it’s better to trust wrong person once, than always distrust all the people

But building trust, despite being central to HC ans CS, is only one - basic - component. Cultural exchange and knowledge sharing are also important, though so far I was unable to comprehend these components sufficiently to write on them.

At the CouchSurfing.com website, it appears to be popular to put some test/quiz results into profiles. These are the tests:

Your Personality is Very Rare (INTP)

Your personality type is goofy, imaginative, relaxed, and brilliant. Only about 4% of all people have your personality, including 2% of all women and 6% of all men You are Introverted, Intuitive, Thinking, and Perceiving.

And two kinda funny Nerd Tests, version 1 and version 2:

develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

Check this project out - you might find that the software you need is already available as Debian package.

This post was stimulated by Steffen’s comment.

I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

This yet has to be fixed somehow.

If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:

- first, install all the necessary packages:
aptitude install build-essential libxml2 libxml2-dev python-dev

- then configure, make and install libsbml:
./configure ––with-python (execute from the directory where the downloaded libsbml archive was extracted to)
make
make install
ldconfig

- then check if installation was successful:
python
and when the python prompt >>> appears, run from libsbml import * - if there are no warnings/errors, then you are done!

One of the solutions work-arounds (suggested by Andre Pirard) is to slow-right-click, that is to hold the right mouse button down until the menu actually appears, then - and only then - release it. Or, you can even slow-right-click, move the pointer over the desired menu item, and then release - that will perform the desired action in a single long right click (instead of more common single right click with a following single left click.)

This bug/behaviour is otherwise unsolved.

Little research had shown that the simplest solution is to disable FireFox’s/IceWeasel’s feature to auto-detect if Internet connection is available: go to about:config, find browser.offline-apps.notify and set it to false. After this, FireFox/IceWeasel 3 will no longer try to check if you have Internet connection.

However, this is not a good solution, because auto-detection generally improves user experience (e.g. by automatically using cached page versions for tabs open at startup). The actual reason (in many cases) is the network detection by the NetworkManager - it reports “no connection” although connection is present (bug report).

The simple solution is to remove NetworkManager.

Another simple solution (without removing NetworkManager) is to disallow NetworkManager to notify other desktop application about the presence of the internet connection (slightly edited):

Open the terminal/konsole (Applications–>Accessories—>Terminal), and type gksudo gedit /etc/dbus-1/system.d/NetworkManager.conf (note: path might differ for your Linux distribution - try locate NetworkManager.conf). Then replace all lines

< allow send_interface="org.freedesktop.NetworkManager"/ >
with
< deny send_interface="org.freedesktop.NetworkManager"/ >

Save the changes and either reboot or just stop/kill/restart the running instance of NetworkManager. This change will stop NetworkManager from notifying FireFox/IceWeasel and other desktop applications about the presence/absence of internet connection - and FireFox will no longer start in Offline mode.

(Thanks Nikitas350 from Ubuntu forums for this fix.)

Personally, I did what Nikitas350 suggested, and also removed the networkmanager-gnome package - I’m still able to add networkmanager-kde monitor to Gnome panel, if I want to (and for me, networkmanager-kde works properly).

The even better solution would be to make NetworkManager detect the availability of connection properly. However, I did not dig deep enough to find how to do that - comments and better solutions are welcome.

One of the more complicated solutions (and still not a perfect one) was also found at Ubuntu forums (slightly edited for contextual clarity):

I am using USB modem to connect to internet and the Offline mode issue was also bothering me after upgrading to Firefox 3.

The solution I have found was: disable Network Applet from System -> Preferences -> Sessions, and add the following lines to the file “/etc/network/interfaces”:

auto eth0
iface eth0 inet dhcp

Thus, I guess, Firefox believes that eth0 (i.e. ethernet card) is active, although Internet connection is established via ppp0 (i.e. USB modem).

Here is formal definition:

high-throughputomics

the term is used to denote/mention any or all of the modern high-throughput techniques (in all of, but not limited to: genomics, transcriptomics, proteomics, …), together with derived/applicable data-processing approaches. All the “networks” things also conveniently fall into the high-throughputomics definition

As this is a general term, it might be even suitable as a conference title (but NOT for ICSB, which I’m waiting for eagerly).

For a shorter and informal (spoken-only) term, putomics can be used:

putomics

spoken-only, informal short form of high-throughputomics

Putomics is also conveniently similar to “computation” (computomics):

computomics

application of computer hardware and software for the analysis of massive amounts of data, obtained using high-throughput methods; this is a research sub-field of high-throughputomics

P.S.
For easier citing:

Tokovenko, Bogdan. New bioinformatics term: high-throughputomics. 2008-07-16. URL:http://bogdan.org.ua/2008/07/16/new-bioinformatics-term-high-throughputomics.html. Accessed: 2008-07-16. (Archived by WebCite® at http://www.webcitation.org/5ZMD9DITU)

What is on offer (mirrors):

• backports.org
• cygwin
• deb.opera.com
• debian - stable, testing, sid
• debian-archive (starting from 1.1!)
• debian-multimedia
• installation media (CDs/DVDs)
• debian-security
• even debian-volatile is here!

All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

Gone editing /etc/apt/sources.list

P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec . I found that ftp2.debian.org.ua mirror is faster at the moment.

It installed and runs fine under Debian Etch:

However, as you could notice from the screenshot above, CPU use is almost 100% while IE6Linux is running. It is better illustrated by the next screen:

I didn’t yet bother finding out what’s wrong, but that must have some kind of a fix, as running at 100% CPU on a laptop is … hot.